Whole-genome chromatin landscape of symbiotic genes

A role for epigenetic and lncRNA regulations to orchestrate symbiotic gene expression inM. truncatula ?

Advances in deciphering the functional architecture of eukaryotic genomes have recently been facilitated by technological advances in sequencing techniques, allowing a more appropriate representation not only of coding genes, but also of repeated elements and non-coding RNAs in genomic sequence assemblies.

Teams from LIPM (Toulouse) and IPS2 (Paris-Saclay) institutes used PacBio sequencing to better assemble the genome of the Medicago truncatula model legume plant (A17 genotype), used in particular for the study of endosymbioses, thus making possible to identify genomic rearrangements between different genotypes at a resolution close to the nucleotide base.

The annotation of this new M. truncatula genome allowed for the first time a global analysis of transposable elements and their dynamics. It was also possible to identify new elements associated with the development of symbiotic nodules, in particular 1037 long non-coding RNAs (lncRNAs) induced in these organs.

It is important to mention that we have also identified that a substantial proportion (~35% and 38%, respectively) of the genes induced in nodules or expressed in their differentiation zone co-localize in genomic "clusters" (270 and 211, respectively), called "symbiotic islands". These islands contain many expressed IncRNA genes and show both differential DNA methylation and histone marks.

Epigenetic regulations and lncRNAs thus seem to be new attractive elements for orchestrating the expression of symbiotic genes in M. truncatula.